That simply doesn't make sense.
Did New 3DS mean games were launched that only worked on it vs orig 3DS?
Did DSi mean games were launched that only worked on it vs DSPhat?
Will there be PS4Pro games that don't work on PS4?
In all those cases there as at least different hardware / revisions. In this case your talking about the exact same console.
No, there will be no games that only work in portable or only docked mode. Docked mode isn't going to be a 5 fold or 10 fold increase in power. Its only going to allow a 720p game be stable and 900p on a TV (or 1080p).
This is a power difference that is likely less than the difference between Xbox One and PS4 now. Think people give too much credit to raw flops and ignore the far more important technical functionality or architecture in a GPU that isn't quantified in a flop.
From everything know thus far, there is no reason to think that any of these games being made could not be put on NS. Yes, they may be 720p vs 900p on XboxOne or 1080p on PS4 and they may or may not have more frame rate drops (granted many cases an XboxOne game is more stable than PS4), but it is certainly possible as the GPU core technology support is the same, just weaker. Whereas in past gens Wii and WiiU both were missing core technology, had contradictory CPU/architecture and were far less in terms of raw power than NS to XboxOne.
See my comparison thread and wait for January. I do believe there will be 3rd party games announced that demonstrate this to be true while not every game is immediately show as being supported due to Nintendo/3rd party relations, but that will change as 3DS is scaled down and NS proves to be a successful platform.